Franchthi Cave, bordering Kiladha Bay, in Greece, is a key archaeological site, due to its long occupation time, from ~ 40,000 to ~ 5000 year BP. To date, no clear evidence of Neolithic human dwellings in the cave was found, supporting the assumption that Neolithic people may have built a village where there is now Kiladha Bay. During the Neolithic period/Early Holocene, wide areas of the bay were indeed emerged above sea level. Bathymetric and seismic data identified a terrace incised by a valley in ~ 1 to 2 m sediment depth. Eight sediment cores, up to 6.3-m-long, were retrieved and analysed using petrophysical, sedimentological, geochemical, and chronostratigraphic methods. The longest core extends into the exposure surface, consisting of a layer of carbonate rubble in a finer matrix, representing weathering processes. Dated organic remains place this unit at ~ 8500 cal year BP. It is overlain by stiff silty mud representing an estuarine environment. This mud is capped by reduced sediments with roots marking an exposure surface. A shell-layer, dated to ~ 6300 cal year BP, overlies this terrestrial sequence, reflecting the marine transgression. This layer occurs at 10.8 mbsl, 7.7 m deeper than the global sea level at that time, suggesting tectonic subsidence in the area. It is overlain by finer-grained marine carbonate-rich sediments. The top of the core shows traces of eutrophication, pebbles and marine shells, all likely a result of modern anthropogenic processes. These results are interpreted in the context of human occupation: the exposed surface contains pottery sherds, one dating to the Early to Middle Neolithic period, indicating that Neolithic people were present in this dynamic landscape interacting with a migrating coastline. Even if the artefacts are isolated, future investigations of the submerged landscape off Franchthi Cave might lead to the discovery of a Neolithic village, which eventually became buried under marine sediments.